Currently, it is estimated there are about 270 to 300 million people worldwide who are infected with hepatitis C virus (HCV), 2.7 to 4 million of those are in the United States. In industrialized countries, HCV accounts for 20% of cases of acute hepatitis, 70% of cases of chronic hepatitis, 40% of cases of end-stage cirrhosis, 60% of cases of hepatocellular carcinoma and 30-40% of liver transplants. The incidence of new symptomatic infections of HCV has been estimated to be 13 cases/100,000 persons annually. For every one person that is infected with the AIDS virus, there are more than four infected with HCV. Currently, 8,000 to 10,000 deaths each year are a result of Hepatitis C (updated Jan. 31, 2006). The CDC (Center For Disease Control) estimates that there are up to 30,000 new HCV infections in the U.S. every year.
About 80% of HCV-infected individuals have no signs or symptoms. In others, the symptom include: jaundice, fatigue, dark urine, abdominal pain, loss of appetite, and nausea. For 55-85% of infected individuals, over the long term, HCV infection persists and become a chronic infection. Of the chronically infected individuals, about 30% develop liver disease.
Hepatitis C virus has six different genotypes. The most prevalent types circulating in the Western countries are sub-genotypes 1a and 1b. In a person with chronic infection, hepatitis C virus reproduces up to 1012 virion each day. Neumann, et al. Science 282:103-107 (1998). This rate of reproduction exceeds the rate of reproduction for human immunodeficiency virus (HIV) by an order of magnitude. The reproduction rate of HCV coupled with the lack of proofreading function by the HCV RNA polymerase results many mutations in HCV sequences.
Treatments for hepatitis C include interferon and ribavirin, both of which are licensed for the treatment of persons with chronic hepatitis C. Interferon can be taken alone or in combination with ribavirin. Combination therapy, using pegylated interferon and ribavirin, is currently the treatment of choice. Combination therapy can get rid of the virus in up to 5 out of 10 persons for genotype 1 and in up to 8 out of 10 persons for genotype 2 and 3.
There are no known vaccines for the prevention of hepatitis C virus infection. Until the present inventors made their discovery herein, the reason as to why individuals with chronic stage HCV infection had weak and ineffective immune responses was poorly understood. The inventors and others have demonstrated that most, if not all of the HCV sequences obtained from persons with HCV infection contain epitope escape variants. As such, the inventors have made a novel and useful discovery that describes, inter alia, the reasons for the observed genetic changes taking place during infection of a human host. These include the tendency of the virus to mutate towards a consensus sequence that is optimal for viral replication and fitness, and the competing tendency of the virus to mutate away from sequences that induce effective immunological responses in particular human hosts. This discovery has important implications for vaccine design.
Several computational alternatives to isolate-based vaccine design exist. One approach is reconstruction of the most recent common ancestor (MRCA) sequence. In this type of analysis, the ancestral state is an estimate of the actual sequence that existed in the past (i.e., it comes directly from the reconstructed history). See Science, 299:1515-1518 (2003). Another type of computational analysis is a center of the tree (COT) approach. The COT approach identifies a point on the unrooted phylogeny, where the average evolutionary distance from that point to each tip on the phylogeny is minimized. Advocates of this approach state that because the COT is a point on the phylogeny, the estimated COT sequence will have the same advantages as the estimated ancestral sequence. See, for example, U.S. Application 2005/0137387 A1. However, this COT approach is sufficiently complex that reducing it to practice for a large and heterologous data set is not practical with technology; specifically, the phylogenetic methods cannot address a sparse data set like the one for HCV, wherein most of the data for any individual sequence are missing. In addition, the premise of the COT approach is that when the phylogenetic tree is unbalanced (dominated by a particular lineage), the COT approach proposed therein provides a more representative sequence than the ancestral sequence. However, the HCV tree has been shown, by the inventors and others, to be balanced and star-like (see Ray S C et al, J Exp Med 2005 Jun. 6; 201(11):1753-9 and Salemi M and Vandamme A, J Mol Evol 2002; 54:62-70). Overall, the MRCA and COT approaches are impractical for application to the HCV sequence database, and their primary justification does not apply.
A third type of computational analysis is the consensus sequence approach. Because the consensus sequence is composed of the amino acid most commonly observed at each position, it likely represents the most fit state of the virus. Thus, effective evasion of the immune response by selection of a sequence divergent from consensus may result in a less fit virus from a replicative standpoint. The consensus sequence approach favors heavily sampled sublineages and deemphasizes outliers. The consideration of an unbalanced phylogenetic tree is not important for HCV, because the phylogeny is balanced (star-like). As such, the approaches disclosed herein are far more straightforward than the other types of computational analysis. Furthermore, these approaches can use the entire data set for HCV. One advantage of the consensus sequence is that it minimizes the genetic differences between vaccine strains and contemporary isolates, effectively reducing the extent of diversity by half, and thus it may have enhanced potential for eliciting cross-reactive responses.
A computational method is therefore needed to generate a sequence for use in vaccines that more broadly represents circulating strains, and also restores the immunogenic forms of HCV epitopes. Currently, there is a need for a method to effectively treat individuals who are infected with HCV or exposed to HCV. With the decline in an infected individual's immune system as he/she enters chronic phase, it would be highly desirable to lessen that individual's chances of progressing to the chronic phase by administering a form of treatment during the acute phase of infection. Most chronically infected people are ineligible for the currently available therapies. A vaccine could be used to enhance responses to currently available or future therapies. Further, there is a need for a prophylaxis of HCV infection. The invention disclosed herein meets all these needs and provides even more beneficial uses.
All references, patent, and patent applications cited in this patent application are herein incorporated by reference, each in its respective entirety for all purposes.